Volume 20, Issue 4, Pages 541-548 (April 2013) Chemical Proteomics with Sulfonyl Fluoride Probes Reveals Selective Labeling of Functional Tyrosines in Glutathione Transferases  Christian Gu, D. Alexander Shannon, Tom Colby, Zheming Wang, Mohammed Shabab, Selva Kumari, Joji Grace Villamor, Christopher J. McLaughlin, Eranthie Weerapana, Markus Kaiser, Benjamin F. Cravatt, Renier A.L. van der Hoorn  Chemistry & Biology  Volume 20, Issue 4, Pages 541-548 (April 2013) DOI: 10.1016/j.chembiol.2013.01.016 Copyright © 2013 Elsevier Ltd Terms and Conditions

Chemistry & Biology 2013 20, 541-548DOI: (10. 1016/j. chembiol. 2013 Copyright © 2013 Elsevier Ltd Terms and Conditions

Figure 1 Structures and Labeling Characteristics of Sulfonyl Fluoride Probes (A) Structures of the SF probes used in this study. The DS6B, DS6R, and DAS1 probes contain the AEBSF moiety (gray) with the reactive sulfonylfluoride (S–F). DS6B contains a biotin reporter tag, DS6R a fluorescent rhodamine reporter tag, and DAS1 an alkyne chemical handle for click chemistry. (B) Labeling profiles of DS6R and DS6B are similar in Arabidopsis leaf proteomes. Arabidopsis leaf extract was labeled with and without DS6R or DS6B and either fluorescently labeled proteins were detected from protein gels using fluorescence scanning (left, DS6R), or biotinylated proteins were purified and detected on protein gels using Coomassie blue staining (right, DS6B). ∗, endogenously biotinylated proteins. See also Figures S1 and S2. Chemistry & Biology 2013 20, 541-548DOI: (10.1016/j.chembiol.2013.01.016) Copyright © 2013 Elsevier Ltd Terms and Conditions

Figure 2 Peptide Fragmentation Spectrum Shows Labeling Site of DS6B in AtGST20 (A) The AtGST20 peptide IVAYAAEYR carries the DS6B modification on the first tyrosine. DS6B contains amide bonds that cause fragmentation into DS6B ions with biotin (B), the amin hexanoid acid linker (h), glycine (G), and AEBSF (a). The identified ions are indicated with bars above and below the DS6-modified sequence, as fragments from DS6B and the peptide, respectively. Peptides with an increased mass corresponding to the DS6B modification overlap with the gray bar indicated with an asterisk (∗). The letters correspond to the peaks indicated in (B). (B) Fragmentation spectrum of the DS6B-modified peptide. The letters correspond to the ions indicated in (A). The spectrum and its full assignment are shown in Figure S3. See also Table S1. Chemistry & Biology 2013 20, 541-548DOI: (10.1016/j.chembiol.2013.01.016) Copyright © 2013 Elsevier Ltd Terms and Conditions

Figure 3 SF Probes Target Tyr Residues at Conserved Positions in Four Different GST Classes (A) Overlay of the structure of MmGSTP1 with models of structures of AtGSTU20, MmGSTM1, MmGSTO1, and MmGSTP1. (B) Close-up of Tyr residues that are targeted by SF probes. All these Tyr residues (right) point with their hydroxyl group into the substrate-binding H-site (middle), which is located next to the glutathione-binding G-site (left). For more details, see Figure S5. See also Figure S6 and Tables S2–S4. Chemistry & Biology 2013 20, 541-548DOI: (10.1016/j.chembiol.2013.01.016) Copyright © 2013 Elsevier Ltd Terms and Conditions

Figure 4 SjGST Is Labeled at Y111, as Predicted (A) SjGST is labeled by DS6R. Extracts containing SjGST were heated for 10 min at 85°C or preincubated for 15 min with 500 μM AEBSF or 400 μM DS6B and then labeled with 2 μM DS6R for 15 min at pH 8. Proteins were detected from protein gel by fluorescent scanning and Coomassie blue staining. (B) Crystal structure of SjGST bound to γ-glutamyl[S-(2-iodobenzyl)cysteinyl]glycine (IBG, blue sticks) (1m9b [Cardoso et al., 2003]). The protein surface is shown in gray and the hydroxyl groups of the 14 tyrosines in red. (C) Enlargement of outlined section in (B) showing the substrate-binding cleft with IBG (blue) and the hydroxyl groups (red) of three tyrosines, Y104, Y111, and the catalytic Y7. (D) SjGST is labeled at Y111 by DS6R. E. coli extracts containing 7.5 μg (mutant) SjGST were treated with or without heating (10 min at 85°C) and labeled with 2 μM DS6R for 15 min at pH 8. Proteins were detected from the protein gel by fluorescent scanning and Coomassie blue staining. See also Table S5. Chemistry & Biology 2013 20, 541-548DOI: (10.1016/j.chembiol.2013.01.016) Copyright © 2013 Elsevier Ltd Terms and Conditions

Figure 5 Y111F Substitution in SjGST Affects NBD-Cl Conjugation but Not Glutathione Binding (A) Mutant proteins are able to bind glutathione beads. Glutathione beads were incubated with (mutant) SjGST proteins and washed. Proteins were eluted without (−) and with (+) 10 mM glutathione in the elution buffer, and proteins in the eluate were detected on protein gels by Coomassie blue staining. (B) Y111F mutant is hampered in conjugation of NBD-Cl with glutathione. (Mutant) SjGST proteins were incubated with various NBD-Cl concentrations and the conjugate concentration was determined by measuring the absorbance at 419 nm for 10 min. Error bars indicate the standard deviation of three measurements. The experiment was repeated three times with similar results. (C) Steady-state catalytic parameters of wild-type and mutant SjGST proteins with NBD-Cl as a substrate. The unit used for Vmax is μmol/min/mg protein. Values are given as the mean ± SEM for three independent experiments. Chemistry & Biology 2013 20, 541-548DOI: (10.1016/j.chembiol.2013.01.016) Copyright © 2013 Elsevier Ltd Terms and Conditions